High-throughput characterization of intrinsic disorder in proteins from the Protein Structure Initiative

Derrick E. Johnson, Bin Xue, Megan D. Sickmeier, Jingwei Meng, Marc S. Cortese, Christopher J. Oldfield, Tanguy Le Gall, A. Keith Dunker, Vladimir N. Uversky

Research output: Contribution to journalArticle

26 Scopus citations

Abstract

The identification of intrinsically disordered proteins (IDPs) among the targets that fail to form satisfactory crystal structures in the Protein Structure Initiative represents a key to reducing the costs and time for determining three-dimensional structures of proteins. To help in this endeavor, several Protein Structure Initiative Centers were asked to send samples of both crystallizable proteins and proteins that failed to crystallize. The abundance of intrinsic disorder in these proteins was evaluated via computational analysis using predictors of natural disordered regions (PONDR®) and the potential cleavage sites and corresponding fragments were determined. Then, the target proteins were analyzed for intrinsic disorder by their resistance to limited proteolysis. The rates of tryptic digestion of sample target proteins were compared to those of lysozyme/myoglobin, apomyoglobin, and α-casein as standards of ordered, partially disordered and completely disordered proteins, respectively. At the next stage, the protein samples were subjected to both far-UV and near-UV circular dichroism (CD) analysis. For most of the samples, a good agreement between CD data, predictions of disorder and the rates of limited tryptic digestion was established. Further experimentation is being performed on a smaller subset of these samples in order to obtain more detailed information on the ordered/disordered nature of the proteins.

Original languageEnglish (US)
Pages (from-to)201-215
Number of pages15
JournalJournal of Structural Biology
Volume180
Issue number1
DOIs
StatePublished - Oct 1 2012

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Keywords

  • Intrinsically disordered proteins
  • Limited proteolysis
  • Protein disorder prediction
  • Protein structure initiative

ASJC Scopus subject areas

  • Structural Biology

Cite this

Johnson, D. E., Xue, B., Sickmeier, M. D., Meng, J., Cortese, M. S., Oldfield, C. J., Le Gall, T., Dunker, A. K., & Uversky, V. N. (2012). High-throughput characterization of intrinsic disorder in proteins from the Protein Structure Initiative. Journal of Structural Biology, 180(1), 201-215. https://doi.org/10.1016/j.jsb.2012.05.013